[ome-users] FEI MORE tf8 files sorted to Orphaned Images

[Dominik Lindner (Staff)]

Hi Niko and Kai,

I did some more investigation, and I think the main problem simply is that the metadata contains a plate definition although the file is not supposed to be a plate. There was some discussion going on here as well https://github.com/openmicroscopy/openmicroscopy/pull/4751 (I closed it again, because the PR would introduce other problems). Basically in Insight I have to rely on the metadata, I couldn't find a way to determine that the file is not plate other then checking the metadata. And if it's reported as plate, Insight ignores the Project/Dataset setting, which is reasonable.

Regards,
Dominik


On 14 Jul 2016, at 13:17, Nikolaus Ehrenfeuchter <nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:


Hi Dominik,

Kai and me did some more investigation on this and figured out that the tf8 files will be  placed in the correct location when using the command-line importer instead of insight. Does this give any additional hint?

Cheers
Niko

Am 14.07.2016 2:11 nachm. schrieb "Dominik Lindner (Staff)" <d.lindner at dundee.ac.uk<mailto:d.lindner at dundee.ac.uk>>:
Hi Kai,

sorry, that issue slipped a bit from my attention. Up to now I traced it back to the
OMETiffReader. For these files it reports "High-Content Screening (HCS)", that causes
the Insight importer to ignore the Dataset/Project settings. I'm not sure if that's an
Importer problem, or more a Bioformats issue. I'll have to involve some Bioformats people
into this. Sorry for the late reply.

Cheers,
Dominik


> On 13 Jul 2016, at 13:45, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:
>
> Hi Dominik,
>
> I was just wondering whether you'd already have some news regarding this issue.
>
> I have just tested this problem again with OMERO 5.2.4, but it still persists.
>
> As Niko wrote this is indeed the case for both "regular" TIFFs and tf8 files recorded with the LA software on the FEI MORE.
>
> Thanks and cheers,
> Kai


The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20160720/df07940c/attachment.html>